#!/usr/bin/env python

#this script set up and runs several molecular dynamics trajectories
#this script must be called in the directory containing the n traj folders named as 000n
#a properly formatted Job file is required in the same foulder of the script

#################################################
from os import path, getcwd 			#
from os import chdir, system			#
from shutil import copy				#
#################################################

# Define traj labels ############################
						#
first = 1					#
last  = 1000					#
						#
# Define calculation parameters #################
# this value will be used in the Job file #######
						#
JobName			='160LO'		# Just a general lable: "JobName_NumTraj"
TimeLimit		='50'			# in hours:		"TimeLimit:00:00"
NCores			='16'			#
SubmissionSteps		='200'			#
						#
#################################################

JobName = JobName 

here=getcwd()				#workdir

for i in range(first,(last+1)):

	traj= '%.4d' % i		# define working directory
	newdir=path.join(here, traj)	# updating mypath

	if not path.exists(newdir): 
		print "folder", newdir, "not found. exiting..."
		quit()

	chdir(newdir)			# change workdir

	if not path.exists('Job-erc'):	# otherwise the calculation has already been started sometimes

		copy('%s/INPUTS/checker' 		% here	, 'checker')			# copy the check codes and Jobfile
	        copy('%s/INPUTS/check-CHD3.py' 	% here	, 'check-CHD3.py')		# 
		copy('%s/INPUTS/Job-erc'		% here	, 'Job-erc')			#
		system('cp %s/INPUTS/INCAR* .'		% here )				#
		system('cp %s/INPUTS/POTCAR .'		% here )
		system('cp %s/INPUTS/KPOINTS .'		% here )
		system('cp %s/INPUTS/vdw_kernel.bindat .'		% here )

		lable = traj + '_' + JobName							
		modify = 'sed -e \"s|_JOBNAME_|%s|g\" Job-erc > Job' % lable 		# modify the Jobfile
		system(modify)								#
		modify = 'sed -i \"s|_TIMELIMIT_|%s|g\" Job' % TimeLimit		#
		system(modify)								#
		modify = 'sed -i \"s|_NCORES_|%s|g\" Job' % NCores			#
	       	system(modify)								#
	        modify = 'sed -i \"s|_SUBSTEPS_|%s|g\" Job' % SubmissionSteps		#	
		system(modify)								#

		system('qsub Job > ID.job')	# RUN JOB #######################################
		system('cat ID.job')
	else: print ">>> traj %.4d <<<< already submitted" % i

	chdir('..')								# back to the starting folder